[gmx-users] ATP

[Kay Gottschalk]

Hi there,

my system is a protein with ATP, and I'm using the Gromacs ff. In the 
initial pdb-file, 3 hydrogens are missing, thus Gromacs nicely 
complains about that. If I just leave them out (with the '-missing' 
option), ATP is too negatively charged. Is there any reasonable way to 
build the hydrogens with Gromacs? Unfortunately I don't have Insight 
here, and SwissPDB cannot do it. Alternatively I might increase the 
radius and weight and decrease the charge of the affected oxygens in 
the sense of a 'united atoms ATP', but I'd rather avoid that (the 
dipoles just would be fucked up, and h-bonds will not be able to 
form... ). Help would be appreciated.

Thanks a lot,
Kay.